I have some units assigned to patrol an area and during the patrol I plot a course for one of the units that might take it out of the patrol area will the unit return to the patrol area and resume the patrol on its own after it reaches the reference point I sent it to?
You will have to Un-assign it from the patrol - hotkey 'U', you can do what you need to do and then can re-assign it with a 'Right' click and select mission.
The mission AI may launch a replacement for the now unassigned unit however so be careful.